I'm relatively new to R so bear with me. I'm trying to map gene locations to a chromosome, essentially looking at one chromosome at a time. I have looked at all the useful tools including Gviz, quantsmooth, and even in IdeoViz. The problem is I'm using Oryza sativa as my reference genome, and all of these packages require a separate download usually from UCSC which lacks my reference genome. Is there a way around this problem? I know essentially the length of Chr. 11 and have my data formatted as such.
Gene_ID Chr Start End Annotation Os11t0100600-01 11 14258 16117 Alpha/beta hydrolase family protein. Os11t0103050-00 11 127297 129067 Hypothetical protein.
Is there an easy was to get around this issue? Should I just create a box plot given the range of Chr 11 and then write a for loop to map each of the regions to their given location? I'm just struggling to find the simplest way to do this, so any help would be greatly appreciated.